Protégé 3.4 Release Notes

The contents of this page describe changes relative to the 3.3.1 release of Protégé.

Release Highlights

Database inclusion is now supported!
Major enhancements to Protégé-OWL:
- Direct connection to the Pellet reasoner
- New Protégé-OWL parser with improved performance
- Improved handling of untyped resources
Major enhancements to Protégé Client-Server:
- Huge performance improvements
- Several access policies are now enforced
- User friendly administration of the Protégé server
Improved support for collaborative ontology development

... and many more. Click on the navigation links below to see a complete list of changes.

Important Installation Notes

Do not install this build over an older version. You need to do a clean install for this release to work properly. A "clean install" means that you should either a) install this release into an empty directory, or b) uninstall previous versions of Protégé before installing this release.
Protégé 3.4 requires Java 5.0 (JDK 1.5).
If you have a project in database format in version 3.3.1 and you want to upgrade, you must first convert the project to a file-based one in Protégé 3.3.1 , and then regenerate the database project with Protégé 3.4.
For OWL projects, the format of the PPRJ file (.pprj) has changed in an incompatible way. Protégé 3.4 will be able to read existing PPRJ files, but when these files are saved they will not be properly understood by previous versions of Protégé.
For OWL projects that use the graph widget, please refer to a guide on the wiki for upgrading your project from Protégé 3.3.1 to Protégé 3.4.

Enhancements

Protégé-OWL & SWRL
Core Protégé & Protégé-Frames
Protégé Client-Server
Collaborative Protégé
Bundled Plugins

Bug Fixes

Protégé-OWL & SWRL
Core Protégé & Protégé-Frames
Protégé Client-Server

Enhancements – Protégé-OWL & SWRL

Implemented a new Protégé-OWL parser. The previous version of the Protégé-OWL parser had many problems that made it fragile, perform badly, and use lots of memory. The new parser is much more robust, uses significantly less memory, is much faster, and has better support for untyped resources.
Namespace management has been vastly improved. In previous versions of Protégé, the namespace code was tightly coupled with the underlying OWLModel, which led to many quirks in the way Protégé behaved. Now the namespace management code is a thin layer which defines how the ontology is presented to the user. This release provides better URN support and better xml:base, ontology name, and default namespaces decoupling.
Another important change is that the internal names of the ontology entities are now the fully qualified name, rather than the prefixed name, which may impact application developers. We recommended that developers adapt your code to use full names. The short name is still supported, but may have a performance impact. The support for short names can be disabled, by setting the owlmodel.expand.short.name.in.methods property in the protege.properties file to false. The class edu.stanford.smi.protegex.owl.model.NamespaceUtil provides conversion methods between the full and short names of ontology entities. If you are developing a user interface, we recommended that you display the browser text of an entity, which shows the prefixed name.
Protégé-OWL now has the ability to connect directly to the Pellet reasoner, whereas previous versions only supported connections to an external DIG reasoner. This change includes modifications to the user interface and the API:

UI Changes
- Reasoning functionality is now accessible through the new "Reasoning" menu, which allows users to select from a list of available reasoners. The current choices in this menu are "DIG Reasoner" and "Pellet 1.5.2 (direct)". All reasoning actions such as consistency checking, classification, etc., will work with the selected reasoner.
- It is now possible to query the inferred property values of an individual. This can be done by right-clicking on an individual in the Individuals tab and selecting "Get inferred property values" from the context menu.
API Changes
- The old ProtegeOWLReasoner reasoner interface has been deprecated and the new ProtegeReasoner interface should be used instead. Documentation for accessing the reasoner programmatically using the new interface is available on the Wiki.
- A new plug-in type called a "Reasoner Plug-in" has been introduced that allows developers to plug other reasoners into Protégé-OWL. Currently, there are four implementations of the reasoner plug-in: 1) Jena reasoner, 2) DIG reasoner, 3) Pellet reasoner accessed through the Jena API, and 4) Pellet reasoner accessed through the OWL-API. We have made the DIG reasoner and the Pellet reasoner accessed through OWL-API available through the user interface via the Reasoning menu. Documentation for developing a reasoner plug-in is available on the Wiki.
- The protege-pellet.jar file in the edu.stanford.smi.protegex.owl.inference.pellet folder contains a programmatically accessible Protégé-OWL to OWL-API converter. This allows developers to obtain an OWL-API model from a Protégé-OWL model. The model is a snapshot and not a synchronized (live) copy and the limitations of the conversions are documented in the Javadoc for OWLAPIConverter. We would like to thank clark&parsia for providing an important part of the converter code.
Please note: when using the direct Pellet reasoner with large ontologies, we recommend that users increase the allocation for Protégé-OWL's heap size because Protégé-OWL and Pellet will share the same memory space. In the event that you get an OutOfMemory exception during reasoning, Protégé-OWL will try to recover, but we do not recommend that you try to save your file after this type of exception.
The Individuals tab allows users to add anonymous types to individuals using a button on the Asserted Types panel located under the list of individuals.
Those who use rdfs:label to represent class names now have the ability to put spaces and other characters in class names. In the past, the restriction editor was not very friendly to such users because it could not parse expressions such as "hasTopping some My Favorite Type of Topping". We have modified the grammars used by the restriction editors so that names with spaces can be quoted. For example, the expression above can be represented as "hasTopping some 'My Favorite Type of Topping'".
The OWL restriction and SWRL editors now work with browser text with spaces. Browser text containing spaces will be quoted.
Added support in the Properties tab user interface for creating simple annotation properties.
Made the Help menu more user friendly:
- Combined the "About Protégé..." and "Protégé-OWL Version Info..." menu items into one item called "About Protégé-OWL...". The dialog that results from choosing this menu item no longer has any Protégé-Frames specific text, such as the link to the protege-discussion mailing list.
- Added an item that links to the "Getting Started with Protégé-OWL" page on the Protégé website.
- Added an item that links to the Protégé-OWL FAQ page on the Protégé website.
Added a "merging imports" mode to the Protégé-OWL parser that can be invoked programmatically (default is off), which means that all imports will be merged into one ontology. This feature can be used (if desired) when converting a file-based OWL model to the database backend. In this mode, all imports will be part of the same database table. This is also the way imports used to work prior to build 500 in the 3.4 beta series.
The SWRLTab has been updated to be compatible with Jess version 7.1p1. Compatibility with Jess version 7.0p2 has been maintained.
Improved performance of the SWRL editor when it is used with large ontologies
Updated the query built-ins to SQWRL Built-In Library, which has a number of new built-ins that expand the power of queries.
Added a new XML Query Built-In Library. SQWRL queries can now work directly on XML documents.
Added a new Mathematical Expression Parser Built-In Library. This library allows complex mathematical expressions to be used in SWRL rules or SQWRL queries.
Updated the SWRL Built-In Bridge API. This will require a very minor change to existing libraries implemented using this bridge: Java built-in implementations now take a list of BuiltInArgument rather than Argument objects.
Ontologies with SWRL rules no longer need to explicitly import swrl.owl and swrlb.owl, so the use of SWRLTab-generated OWL files with other tools and reasoners should be easier
Implemented negative operators in the SWRLTab temporal built-in library.
Annotation values can now be used to refer to OWL classes, properties, and individuals in SWRL rules.
In the Individuals tab, searches are now performed using the browser text of the individuals.
Added support for searching of OWL entities using synonym properties, which can be any annotation property that takes a literal as a value. Configuration for the search synonym properties is accessible in the OWL menu under Preferences -> Searching.
Added support in the native writer for SWRL rules.
Modified the SWRLTab and the SWRL Jess Bridge to support inference over larger ontologies.
SWRL system classes are now hidden from the user interface by default.
The SWRLTab now works with the OWL database back-end.
Added a mechanism to disable automatic importing of several ancillary ontologies by the SWRLTab.
Improved the performance of the OWL file to OWL database conversion.
The display of inferred types in the Individuals tab can be now configured to a) show all types (default), or b) show direct types only. Instructions for configuring the second option are available on our Wiki.
There is a new option available for code generation to include prefixes in the generated Java names. This option is configurable via Code | Generate Protege-OWL Java Code... | Include prefixes in generated Java names.
The Java Code Generator now generates getXXXProperty methods on Factory classes.
The restriction editor finder now uses the same finder as the class tree. This means that users will no longer have to add a "*" in front of the search string.
It is now possible to export an OWL/RDF database project to a file using the native writer from the File | Export menu item.
The triples table, which is accessible by a switch icon in the Annotations widget, shows all triples that have the selected resource as a subject. In previous versions, the triples were filtered.
The Add type button in the OWL Individuals tab is now disabled if no individual is selected.
Added a getIndividualDirectTypes method to the reasoning interface (ProtegeReasoner) for getting the direct inferred types of an individual.
Added a method in the OWLModel interface for creating simple annotation properties.
Added an addRepository() method in the OwlProjectFromUriCreator, which can be set prior to parsing.
Added a getHasValues(RDFProperty) method to the OWLNamedClass interface.

Enhancements – Core Protégé & Protégé-Frames

Project inclusion is now supported in database mode!
Made two changes that improved the performance of the Instances tab:
- Added the ability to disable the display of instance counts in the Class Hierarchy pane. Normally, Protégé displays the number of instances for each class in the class hierarchy in parenthesis next to the class name. This was causing problems when users clicked on a class with thousands of subclasses because calculating the number of instances for each of the subclasses was taking too much time. To disable the display of instance counts, go to Project | Configure... | Options and check the box next to "Suppress Instance Count Display".
- The pane in the Instance Browser that displays instances of a particular class is now multithreaded. If a user selects a class that has thousands of instances, viewing those instances in the Instance Browser is much faster.
Archive and Revert functionality now works for database projects. "Archive" will create a copy of the current version of the ontology in a new database table. "Revert" will override the current table with the contents of a previously versioned table. Please note: this is not yet working for PostgreSQL.
Introduced code generation capability for Protégé-Frames, accessible from the "Code" menu. Works with both file and database back-ends.
Added support for the Derby database (many thanks to Mike Smith!!).
Two new slot widgets called "EditorPane" and "EditorPanePlain" have been added to the standard distribution. These widgets allow rendering and editing of slot values as HTML text, which facilitates the inclusion of links as part of a slot value. Documentation is available on the Wiki:

http://protegewiki.stanford.edu/index.php/EditorPanePlain
http://protegewiki.stanford.edu/index.php/EditorPane
The RDF back-end now also works with RDF projects stored in JAR files.
Removed dependencies on the "looks.jar" file. Applications that only use the Protégé APIs no longer need to include looks.jar on the classpath.
In the Queries tab, the export functionality now quotes values if delimiters are used in slot values.
The list of display slots in the Forms tab is now sorted alphabetically.
Added methods in ProjectView for reloading only one tab, or reloading all tabs except one.
The position information for nodes in the graph widget that is stored in included projects is now available in including projects. This was a limitation in previous versions of Protégé.
Users can now pass arguments to Protégé's main method in the form of -propMyProp=MyValue, where -prop is the prefix for all property-value assignments. These properties are accessible in the same way as properties from the protege.properties file.
When exporting a Protégé-Frames project to OWL, users now have the option of choosing the native OWL writer rather than the default Jena writer. Please note that there is a known limitation if using the native writer: Protégé-Frames projects that contain PAL constraints are not exported correctly. If your project has PAL constraints, please continue to use the default writer.
Added search support for multiline string values in the Protégé user interface and in the Protégé API.
Added some utility methods in SystemUtilities for getting system properties.

Enhancements – Protégé Client-Server

New and improved documentation is available on our wiki: http://protegewiki.stanford.edu/index.php/Protege_Client-Server_Tutorial.
Client-server compression is working! This can provide a 10x reduction in network traffic between a Protégé client and the server. Compression is turned on by default.
A new administrative user interface for the Protégé server is available. You can access this UI through the server login panel if the "Administer server" check box is selected. Examples of functionality available through the administrative UI are:
- Ability to see a list of all server sessions. A user with the appropriate permissions can kill other users sessions.
- Ability to see a list of all server projects and project status (ready, shutting down, closed for maintenance).
- Selecting a server project allows you to view statistics such as connected users, cache hit rate, server backlog, and transaction status.
- Server projects can be shut down for maintenance without stopping the Protégé server. When a project is shut down on the server, several notifications are sent to connected clients. Shutdowns can be scheduled to happen in a certain time interval and can also be cancelled if necessary.
- The "Control" tab allows users with appropriate permissions to shut down the Protégé server.
- Detailed documentation of the adminstrative user interface is available on our wiki.
We updated the metaproject ontology. Instances of the server class allow addition of policies that apply to the server as a whole. Existing metaprojects will be updated automatically when the server starts and no information will be lost. After the metaproject updates, we recommend that you change the layout of the Server class in the Forms tab to be the same as that of the Project class. This will make it easier to edit server policies.
New policies enforced in the user interface and API are:
- Administer server
- Kill other users' sessions
- Project shutdown
- Project start
- Server shut down
The read-only policy is now enforced in client-server mode. Users without write access to an ontology will not be able to perform edits. Note that the read-only policy is only enforced if there is a "Write" operation defined in the metaproject.
Clean shutdown of clients if remote projects are shut down.
Clean shutdown of clients if the server connection is lost. A dialog box will inform clients of the lost connection.
It is now possible to export a remote OWL/RDF project stored on a Protégé server to a client using the File | Export menu item.
Performance of the Protege server on multiprocessor systems is vastly improved.
New methods are available in the RemoteServer interface for server administration.
A full API for accessing information in the Metaproject, which is used to configure the Protégé server, is now available in the edu.stanford.smi.protege.server.metaproject package.
Added support in client-server mode for included forms and browser text for Frames projects. The forms for included projects are now also visible in the including project. This was a limitation in previous versions of Protégé.
There are some new startup options that allow Protégé clients to connect directly to a Protégé server:
- -server.user=xxx
- -server.password=xxx
- -server.host=xxx
- -server.project=xxx
Added support for loading projects from HTTP addresses.
Added utility methods for managing projects on the Protégé server.
Optimized performance of the OWL Individuals tab (not the Instances Tab!) in client-server mode for classes with large number of individuals that have browser slots configured. The MultiResourceWidget now uses a different structure for retrieving property values from the server that contains among other things, the individual and the browser text. This means that computation of the browser text can now be done on the server, thus preventing multiple calls across the network. Performance of the OWL Individuals tab is also much improved by using the compression mentioned above. Finally, we optimized several parts of the UI code to minimize the number of network calls.
Added debug and performance monitoring support in the Protégé logger for client-server mode. More information is available on the wiki.
Improved performance of the Lucene Query Tool in client-server mode.
The expression root and the operands of OWLNAryClass are computed on the server, which improves performance.
The server now logs Protégé information to the console, e.g., build number, heap size, character encoding, etc.
The server now saves server projects before shutdown, i.e., through the Administer Protégé Server panel.

Enhancements – Collaborative Protégé

Updated user's guide is available on the wiki: http://protegewiki.stanford.edu/index.php/Collaborative_Protege.
Made the following improvements to the user interface:
- "Reply" and "New Thread" icons were replaced with buttons (users felt that icons were not intuitive enough).
- The word "annotation" was replaced throughout with "notes", which we feel is more user-friendly.
- Panels in the collaboration tab were renamed to Entity notes, Ontology notes, All notes, Search, and Chat.
- The All notes panel shows an overview of all notes in the ontology (ontology & entity notes grouped by entity). This will allow users to see all notes, even if they are "hidden" somewhere deep in the class hierarchy.
- Collaboration tabs now have a refresh button that reloads all notes in the tab. This is similar to "Check Mail" functionality in email clients.
- Notes are now shown in chronological order.
- The Collaboration User's Guide is now accessible via a menu item.
Easier activation of the collaboration panel is now possible using the "Collaboration" menu. Users can can show/hide the panel at any time during a Protégé work session.
It is no longer necessary to activate the Changes tab to create the Changes and Annotations ontology (ChAO). The ChAO will be created automatically (if not already present) when users activate the collaboration panel via the Collaboration menu.
Improved performance of the collaboration features in client-server mode by caching notes on the client-side.
Users can now configure which collaborative tabs (annotations, changes, chat, search, etc.) they would like to see displayed in the user interface. Configuration is accessible from the Collaboration | Configure menu item. See the Collaborative Protégé documentation for more information.
The Chat tab now supports text in HTML format (Bold, Italics, Underline, Strikethrough). Hyperlinks to Web pages can be followed by clicking on them in the chat window.
In the Chat tab, users are able to reference (in a chat message) an internal entity from the ontology by using the syntax @'EntityName' (e.g., @'Pizza'). Clicking on the internal link will bring up a window showing the ontology entity.
The Chat tab now displays a list of the users that are currently online (when running in client-server mode).
The search results panel on the Search tab now contains an additional button to show the annotated entity from the user ontology.
The Changes and Annotations Ontology (ChAO) used by the Changes Tab and Collaborative Protégé to store change tracking and annotation information can now be stored in a database. We have documented how to convert an existing ChAO from the RDF file-based back-end to the database back-end on the wiki.
The same ChAO project can now be shared by more than one project. For example, the CollaborativePizza and CollaborativeNewspaper projects may share the annotation_PizzaNewspaper.pprj project. There is also no longer a requirement that the ChAO project name start with "annotation".
When a user enables the Changes Tab for the first time, she will be asked what type of ChAO project she wants to create. She can choose between:
- RDF back-end (previous setup and default option)
- Database back-end
- Associate an existing ChAO project
The Change menu has several new items:
- Show Changes Ontology Details (e.g., location, back-end, number of annotations and changes)
- Browse Changes Ontology
- View Change Statistics and Conflicts (e.g., the editing conflicts between users)
A new Changes and Annotations API provides full access to the changes and annotation instances stored in a ChAO knowledge base. We have documented this new API on the wiki.
It is now possible to extend the set of existing annotation types (Comment, Advice, Proposal, etc.) from ChAO with custom annotation types, simply by creating a subclass of the Annotation class in the ChAO project. You may add your own properties/slots to the new annotation type and customize its user interface form. Collaborative Protégé will automatically pick up this new annotation type and show it in the available annotation types combo box in the user interface.
All annotations defined in ChAO now have a subject slot attached to them. An automatic backwards compatibility fix is provided for previous versions of the ChAO.
The forms for annotations in ChAO have been updated to more closely resemble a send email form. Users may now enter HTML styles in the body of the annotations and internal links to entities in the ontology.
The creation of annotations will show a dialog that will allow users to post or cancel a message. In previous versions, when the user clicked on the create annotation button, a new annotation was created automatically. Now users have the chance to cancel submission of the new annotation.
All annotations are now rendered with a type specific icon so that they can be more easily distinguished in the user interface. For example, a comment will have a little "c" in its icon, a proposal will have a "P", and so on.
Rename events now are shown as one aggregated change in the Changes tab and the collaboration panel.
Added more checks to determine an absence of changes and to determine if the annotations project is present in the changes and annotations API.
The language of change descriptions in the Changes Tab has been improved so that users can more easily understand the change history of a particular resource.
More checks are made in client-server mode for an improperly configured changes and annotations ontology (ChAO) in the metaproject.

Enhancements – Bundled Plugins

The Jambalaya visualization plug-in has been updated to version 2.7.0, which has many new features and improvements. Searching has never been easier with a new quick search toolbar at the top of the view to help users find classes and instances. Jambalaya also now supports a document management system which lets the user associate documents or URLs with individual nodes. As a result, if there are any files, images, websites etc., that are related to a class or instance, the user can quickly preview those documents embedded right inside Jambalaya. Other new features include more support for custom node shapes, colors, borders, and images. Visit the Jambalaya website for a full list of all the new features and to peruse the user manual.
Bundling a new plug-in called the MetaAnalysis plug-in, which calculates various metadata for ontologies and facilitates the export of that metadata to the Ontology Medata Vocabulary. Documentation for this plug-in is available on our wiki.
Bundling an updated version of DataMaster (version 1.3.1), which is a plug-in for importing schema structure and data from relational databases into Protégé.
Bundled an updated version of the Protege Script Console (build 0.32), which is a tab that provides a scripting environment within Protégé for manipulating an ontology.

Bug Fixes – Protégé-OWL & SWRL

Fixed a bug that prevented users from adding an owl:equivalentProperty to another property via user interface. This can now be done in the Properties Tab:
- switch the Annotations table to the triples view
- click on the "Add existing resource as value" icon
- select the owl:equivalentProperty property
Fixed a bug in sqwrl:count built-in, which caused it to produce inconsistent counts.
The Properties tab now appears correctly even if an ontology contains properties that are both datatype and object properties (making the ontology OWL Full). This limitation previously caused problems with the display of FOAF vocabulary properties.
SWRL and SWRLB entities are now filtered from the DIG translation, which caused some reasoners to report warnings or errors.
Fixed a problem that caused some widgets in the Individuals tab to be disabled. Users were not able to add new values to properties attached to individuals.
Fixed the display of symmetric, transitive, and inverse functional properties that do not have owl:ObjectProperty as a declared type.
Bug fix for "Compute inferred types" for the Pellet implementation of the direct reasoner (available in the GUI via the context menu) to return all the types of an individual rather than just the direct types.
Fixed a bug for the conversion of owl:differentFrom in the implementation of the direct Pellet reasoner that caused an error message to be displayed at reasoning time: "Error at synchronization:edu.stanford.smi.protegex.owl.model.DefaultOWLAllDifferent".
Removed a warning from the console when using the triples view for individuals.
Fixed a bug in the OWLDateWidget that was preventing users from being able to change the value of the date.
Fixed a bug that caused type information to be lost for some inferred data property values.
Fixed a serious bug in the restriction editor that could lead to ontology corruption.
Fixed a problem with the file browser for local folder repositories.
Fixed a problem with getHasValuesOnTypes method in the RDFIndividual interface.
The parser uses a new algorithm to compute orphan classes. This fixes the cases in which certain classes did not show up in the classes tree.
Fixed a problem in the conversion of projects from one storage format to another.
Fixed a problem with the OWL Wizard for creating multiple individuals.
Several fixes for the Protégé-OWL code generator. The generated getXYZ(String name) methods in the factory will return null if the name of the individual passed as the argument does not have the right ontology type.
Fixed a bug in the parser that could lead to data corruption in a small number of cases for OWL ontologies that contain metaclasses.
Fixed an issue that could silently cause data corruption when using the native writer in combination with sorting ontology contents.
Added a fix for possible name conflict problems at parse time (e.g., if you import an OWL file into a OWL database) by using a random number generator for the anonymous class and individual names.
Added a fix for the native writer that saves each import with its own namespace.
Creating a subproperty will now create a property that has all the types of the super-property.
Fixed several refresh problems in the UI that occurred after renaming an entity (this applies to both Frames and OWL), changing the range of a datatype property, etc.
Fixed a problem in the OWL Properties tab that made properties appear twice when designating a property as functional.
Fixed some memory leaks when disposing a project.
Fixed some bugs that could involve data loss, including a) values of sub data properties can be lost when an OWL ontology is parsed, and b) database import of projects with individuals can become corrupted.
Fixed an issue with the native writer choosing the wrong file encoding for imported files. This sometimes caused data corruption when the imported files contained UTF-8 characters.
Several fixes for the Properties tab, namely that when users create inverse properties, domain and range information is not inverted as well.
Fixed problems with slow searching in the OWLClasses tab.
Previously, Protégé-OWL reported certain property values more than once. Since OWL property values are sets, not multi-sets, this was problematic. A new flag allows constraint of all values to sets, hence removing duplicates.
Parser fixes for classes that are types of themselves and for untyped resources.
Fix for a low level call that caused SPARQL queries to throw occasional exceptions.
Fixed a bug in SWRL's rule group handling.
Fixed an exception was sometimes thrown when a disjoint class was removed in the user interface.
Fixed domain and range widgets that prevented a domain and range from being added to an imported property.
Fixed the range widget that sometimes prevented the addition of a new data range value because the add icon was disabled.
Fixed a problem where a clone operation rearranged the imports tree.
Implemented a fix for DIG's translation of boolean properties. Thanks go to Thomas Russ for suggesting the fix.

Bug Fixes – Core Protégé & Protégé-Frames

The database back-end now works with entity names longer than 255 characters, and several problems have been solved related to ontologies that have two entities with identical names - one capitalized and one with small letters.
Fixed a bug in the database back-end, which prevented users from working with Microsoft SQL Server.
Fixed a bug in the graph widget – when nodes were removed rather than deleted from the graph, the slot that users designated to hold transitions was not being updated.
Fixed a bug in the graph widget that was causing nodes to be drawn behind the palette when users added exisiting instances to the graph.
Fixed a memory leak in the database mode.
Fixed a problem with the Frames HTML export functionality related to the export configuration file not being found.
Fixed a bug where duplicate child nodes appeared in the class tree (or any other tree that uses LazyTreeNode). Many thanks go to Bob Dionne for the fix.
Protégé now escapes the slot and slot value delimiters in the query results file exported from the Queries tab. Again, thanks go to Bob Dionne for the fix.
Fixed a problem where users ran out of Java PermGen space.
Fixed a problem in the installer that caused Protégé to get installed with an empty program group on the Windows Vista operating system.

Bug Fixes – Protégé Client-Server

Fixed some refresh problems when an entity (class, property, individual) was renamed in the user interface.
The insertion order is now preserved when calculating the value closure for slots.
Fixed some issues with inherited browser slot patterns. In previous versions, the browser slot patterns were not always inherited by subclasses.
Fixed a problem that prevented preservation of default view annotations.